1V08

Crystal structure of the Zea maze beta-glucosidase-1 in complex with gluco-tetrazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E1EPDB ENTRY 1E1E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.522% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8957.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.18α = 90
b = 104.8β = 90
c = 119.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002001-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9529.896.60.0726.93.392037
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.01940.4561.53.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E1E1.929.758735246041000.1750.1730.205RANDOM22.38
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.382.88-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.98
r_scangle_it2.341
r_scbond_it1.413
r_angle_refined_deg1.189
r_mcangle_it0.908
r_angle_other_deg0.895
r_mcbond_it0.475
r_nbd_other0.237
r_symmetry_hbond_refined0.213
r_symmetry_vdw_other0.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.98
r_scangle_it2.341
r_scbond_it1.413
r_angle_refined_deg1.189
r_mcangle_it0.908
r_angle_other_deg0.895
r_mcbond_it0.475
r_nbd_other0.237
r_symmetry_hbond_refined0.213
r_symmetry_vdw_other0.206
r_nbd_refined0.2
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.178
r_chiral_restr0.097
r_nbtor_other0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7934
Nucleic Acid Atoms
Solvent Atoms839
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing